Construction of the Classification Model Using Key Genes Identified Between Benign and Malignant Thyroid Nodules From Comprehensive Transcriptomic Data

Thyroid nodules are present in upto 50% of the population worldwide, and thyroid malignancy occurs in only 5–15% of nodules. Until now, fine-needle biopsy with cytologic evaluation remains the diagnostic choice to determine the risk of malignancy, yet it fails to discriminate as benign or malignant in one-third of cases. In order to improve the diagnostic accuracy and reliability, molecular testing based on transcriptomic data has developed rapidly. However, gene signatures of thyroid nodules identified in a plenty of transcriptomic studies are highly inconsistent and extremely difficult to be applied in clinical application. Therefore, it is highly necessary to identify consistent signatures to discriminate benign or malignant thyroid nodules. In this study, five independent transcriptomic studies were combined to discover the gene signature between benign and malignant thyroid nodules. This combined dataset comprises 150 malignant and 93 benign thyroid samples. Then, there were 279 differentially expressed genes (DEGs) discovered by the feature selection method (Student’s t test and fold change). And the weighted gene co-expression network analysis (WGCNA) was performed to identify the modules of highly co-expressed genes, and 454 genes in the gray module were discovered as the hub genes. The intersection between DEGs by the feature selection method and hub genes in the WGCNA model was identified as the key genes for thyroid nodules. Finally, four key genes (ST3GAL5, NRCAM, MT1F, and PROS1) participated in the pathogenesis of malignant thyroid nodules were validated using an independent dataset. Moreover, a high-performance classification model for discriminating thyroid nodules was constructed using these key genes. All in all, this study might provide a new insight into the key differentiation of benign and malignant thyroid nodules.

Predicting RNA 5-Methylcytosine Sites by Using Essential Sequence Features and Distributions

Methylation is one of the most common and considerable modifications in biological systems mediated by multiple enzymes. Recent studies have shown that methylation has been widely identified in different RNA molecules. RNA methylation modifications have various kinds, such as 5-methylcytosine (m5C). However, for individual methylation sites, their functions still remain to be elucidated. Testing of all methylation sites relies heavily on high-throughput sequencing technology, which is expensive and labor consuming. Thus, computational prediction approaches could serve as a substitute. In this study, multiple machine learning models were used to predict possible RNA m5C sites on the basis of mRNA sequences in human and mouse. Each site was represented by several features derived from k -mers of an RNA subsequence containing such site as center. The powerful max-relevance and min-redundancy (mRMR) feature selection method was employed to analyse these features. The outcome feature list was fed into incremental feature selection method, incorporating four classification algorithms, to build efficient models. Furthermore, the sites related to features used in the models were also investigated.

Faulty Line Selection Method Based on Comprehensive Dynamic Time Warping Distance in a Flexible Grounding System

A flexible grounding system is a system in which the neutral point of the power supply is grounded via the arc suppression coil in parallel with a low-resistance resistor. When operating normally or a temporary ground fault occurs, the arc suppression coil is used for grounding, whereas the small resistance is switched on when a permanent ground fault occurs. At present, the problem of low protection sensitivity when a high-resistance ground fault occurs in a flexible grounding system has not been solved yet. According to the characteristics of low waveform similarity between the faulty line and the non-faulty line when a single-phase grounding fault occurred, a new faulty line selection method based on a combination of Dynamic Time Warping (DTW) distance and the transient projection method is proposed in this paper. Firstly, the fault transient signal is extracted by a digital filter as a basis for faulty line selection. Secondly, the transient zero-sequence current of each line is projected onto the busbar transient zero-sequence voltage, and the projected DTW distance of each line is calculated. Finally, according to the calculation formula of waveform comprehensive similarity coefficient, the Comprehensive DTW (CDTW) distance is obtained, and the top three CDTW distance values are selected to determine the faulty line. If the maximum value is greater than the sum of the other two CDTW distance values, the line corresponding to the maximum value is judged as the faulty line; otherwise, it is judged as a busbar fault. The simulation results based on MATLAB/Simulink and field data test show that the method can accurately determine the faulty line under diverse fault conditions.

A Novel Framework Based on Deep Learning and ANOVA Feature Selection Method for Diagnosis of COVID-19 Cases from Chest X-Ray Images

Background and Objective. The new coronavirus disease (known as COVID-19) was first identified in Wuhan and quickly spread worldwide, wreaking havoc on the economy and people’s everyday lives. As the number of COVID-19 cases is rapidly increasing, a reliable detection technique is needed to identify affected individuals and care for them in the early stages of COVID-19 and reduce the virus’s transmission. The most accessible method for COVID-19 identification is Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR); however, it is time-consuming and has false-negative results. These limitations encouraged us to propose a novel framework based on deep learning that can aid radiologists in diagnosing COVID-19 cases from chest X-ray images. Methods. In this paper, a pretrained network, DenseNet169, was employed to extract features from X-ray images. Features were chosen by a feature selection method, i.e., analysis of variance (ANOVA), to reduce computations and time complexity while overcoming the curse of dimensionality to improve accuracy. Finally, selected features were classified by the eXtreme Gradient Boosting (XGBoost). The ChestX-ray8 dataset was employed to train and evaluate the proposed method. Results and Conclusion. The proposed method reached 98.72% accuracy for two-class classification (COVID-19, No-findings) and 92% accuracy for multiclass classification (COVID-19, No-findings, and Pneumonia). The proposed method’s precision, recall, and specificity rates on two-class classification were 99.21%, 93.33%, and 100%, respectively. Also, the proposed method achieved 94.07% precision, 88.46% recall, and 100% specificity for multiclass classification. The experimental results show that the proposed framework outperforms other methods and can be helpful for radiologists in the diagnosis of COVID-19 cases.

Motor Imagery EEG Decoding Based on New Spatial-Frequency Feature and Hybrid Feature Selection Method

Feature extraction and selection are important parts of motor imagery electroencephalogram (EEG) decoding and have always been the focus and difficulty of brain-computer interface (BCI) system research. In order to improve the accuracy of EEG decoding and reduce model training time, new feature extraction and selection methods are proposed in this paper. First, a new spatial-frequency feature extraction method is proposed. The original EEG signal is preprocessed, and then the common spatial pattern (CSP) is used for spatial filtering and dimensionality reduction. Finally, the filter bank method is used to decompose the spatially filtered signals into multiple frequency subbands, and the logarithmic band power feature of each frequency subband is extracted. Second, to select the subject-specific spatial-frequency features, a hybrid feature selection method based on the Fisher score and support vector machine (SVM) is proposed. The Fisher score of each feature is calculated, then a series of threshold parameters are set to generate different feature subsets, and finally, SVM and cross-validation are used to select the optimal feature subset. The effectiveness of the proposed method is validated using two sets of publicly available BCI competition data and a set of self-collected data. The total average accuracy of the three data sets achieved by the proposed method is 82.39%, which is 2.99% higher than the CSP method. The experimental results show that the proposed method has a better classification effect than the existing methods, and at the same time, feature extraction and feature selection time also have greater advantages.